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Structural Properties of the Nickel Ions in Urease: Novel Insights Into the Catalytic and Inhibition Mechanisms

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Structural Properties of the Nickel Ions in Urease: Novel Insights Into the Catalytic and Inhibition Mechanisms Coordination Chemistry Reviews 190–192 (1999) 331–355 www.elsevier.com/locate/ccr Structural properties of the nickel ions in urease: novel insights into the catalytic and inhibition mechanisms Stefano Ciurli a,*, Stefano Benini b, Wojciech R. Rypniewski b, Keith S. Wilson c, Silvia Miletti a, Stefano Mangani d a Institute of Agricultural Chemistry, Uni6ersity of Bologna, Viale Berti Pichat 10, I-40127 Bologna, Italy b European Molecular Biology Laboratory, c/o DESY, Notkestraße 85, D-22603 Hamburg, Germany c Department of Chemistry, Uni6ersity of York, Heslington, York YO15DD, UK d Department of Chemistry, Uni6ersity of Siena, Pian dei Mantellini 44, I-53100 Siena, Italy Accepted 13 March 1999 Contents Abstract.................................................... 331 1. Biological background ......................................... 332 2. Spectroscopic investigations of the urease active site structure .................. 333 3. Crystallographic studies of the native enzyme ............................ 334 4. Crystallographic studies of urease mutants.............................. 341 5. Crystallographic studies of urease–inhibitor complexes ...................... 345 6. Crystallographic study of a transition state analogue bound to urease.............. 348 7. A novel proposal for the urease mechanism ............................. 350 References .................................................. 353 Abstract This work provides a comprehensive critical summary of urease spectroscopy, crystallogra- phy, inhibitor binding, and site-directed mutagenesis, with special emphasis given to the Abbre6iations: JBU, jack bean urease; KAU, Klebsiella aerogenes urease; BPU, Bacillus pasteurii urease; b-ME, b-mercaptoethanol; PPD, phenylphosphorodiamidate; AHA, acetohydroxamic acid; XAS, X-ray absorption spectroscopy; EXAFS, extended X-ray absorption fine structure; CD, circular dichroism; MCD, magnetic circular dichroism. * Corresponding author. Tel.: +39-051-259794; fax: +39-051-243362. E-mail address: [email protected] (S. Ciurli) 0010-8545/99/$ - see front matter © 1999 Elsevier Science S.A. All rights reserved. PII: S0010-8545(99)00093-4 332 S. Ciurli et al. / Coordination Chemistry Re6iews 190–192 (1999) 331–355 relationships between the structural features of the Ni-containing active site and the physico–chemical and biochemical properties of this metallo-enzyme. In addition, the recently determined structure of a complex between urease and a transition state analogue is discussed as it leads to a novel, thought-provoking proposal for the enzyme mechanism. © 1999 Elsevier Science S.A. All rights reserved. Keywords: Urease spectroscopy; Site-directed mutagenesis; Inhibitor binding 1. Biological background Urea is formed in large quantities as a product of catabolism of nitrogen-contain- ing compounds, each human producing, for example, ca. 10 kg of urea per year [1]. Urea spontaneously decomposes with a half-life of ca. 3.6 years [2], and without an efficient degradation process, it would rapidly accumulate causing severe environ- mental problems. The biological catalyst for the hydrolytic decomposition of urea is the enzyme urease (urea aminohydrolase E.C. 3.5.1.5). Urease may be thought to represent the paradigm in the development of biological inorganic chemistry. The first enzyme to be crystallized, from the plant source Cana6alia ensiformis (jack bean) [3], was also the first protein shown to contain nickel in the active site [4]. This discovery stimulated efforts to unravel the chemistry of such a rare microele- ment in other biological settings, leading to the discovery of the presence of nickel in CO–dehydrogenase from photosynthetic bacteria [5], methyl coenzyme M reduc- tase-bound factor Ni-F430 from methanogenic bacteria [6,7], bacterial Ni,Fe–hy- drogenase from several microorganisms [8], acetyl–CoA synthase from methanogenic and acetogenic bacteria [9], and superoxide dismutase from actino- mycetes [10,11]. Urease catalyzes the hydrolysis of urea in plants, algae, fungi, and several microorganisms [12,13], in the final step of organic nitrogen mineralization to produce ammonia and carbamate. This process occurs 1014 times faster than the uncatalyzed reaction [14], with a half-time in the order of microseconds. The carbamate produced during this reaction spontaneously decomposes, at physiologi- cal pH, to give a second molecule of ammonia and bicarbonate [13–16]. The hydrolysis of the reaction products causes an abrupt overall pH increase, the major cause for the negative side effects of the action of urease both for human and S. Ciurli et al. / Coordination Chemistry Re6iews 190–192 (1999) 331–355 333 animal health, and for agriculture. Urease serves as a virulence factor in human and animal infections of the urinary and gastrointestinal tracts, being involved in kidney stone formation, catheter encrustation, pyelonephritis, ammonia encephalopathy, hepatic coma, and urinary tract infections [13,16,17]. The ureolytic activity of Helicobacter pylorii is also the major cause of pathologies (including cancer) induced by gastroduodenal infections by such microorganisms. In another context, urea is largely used worldwide as a soil fertilizer, representing a fundamental source of nitrogen for plant nutrition [18]. This is made possible by the large amount of urease in soil, present both in living ureolytic bacteria [19] and as extracellular urease. The latter is found aggregated with clays and humic substances, which prevent its degradation by extracellular proteolytic enzymes and microorganisms [20–22]. The efficiency of soil nitrogen fertilization with urea is severely decreased by this widespread urease activity, which causes the release of large amounts of ammonia in the atmosphere and further induces plant damage by ammonia toxicity and soil pH increase, thereby posing significant environmental and economic problems [21]. In conclusion, the health and environmental impact of urease activity is enor- mous, and control of the rate of urea hydrolysis by using urease inhibitors would lead to enhanced efficiency of urea nitrogen uptake by plants and to improved therapeutic strategies for treatment of infections by ureolytic bacteria. Several classes of molecules (di-phenols, quinones, hydroxamic acids, phosphoramides and thiols) have been tested as urease inhibitors in medicine [13,16,23]. Urease in- hibitors have also been proposed to control urea hydrolysis in soil [13,24–31]. In particular, phosphoramides have received considerable attention as urease in- hibitors [27,30], the best example being N-(n-butyl)thiophosphoric triamide (NBPT) [32–37]. However, the efficiency of the presently available inhibitors is low, and negative side effects on humans [13,16,38,39] and on the environment [13,40] have been reported. The discovery of urease inhibitors has so far relied upon extended screen tests [41]. A structure-based molecular design approach for the discovery of new and efficient urease inhibitors relies upon the elucidation of the structure of the active site of this enzyme and of its mechanism. The highly conserved amino acid sequences of all known ureases [16,42] and the constant presence of two Ni ions and of their ligands in the active sites [14] infer a common catalytic pathway. Therefore, the determination of the structure of ureases isolated from different sources will establish the essential common features of these enzymes. These analogies will provide a better understanding of the chemistry of the catalysis, and also allow rational design of inhibitors capable of functioning with a broad range of microbial ureases. 2. Spectroscopic investigations of the urease active site structure The presence of six-coordinate octahedral Ni(II) in jack bean urease (JBU) was first proposed on the basis of optical absorption spectroscopic studies [4,43,44], which almost completely ruled out the presence of four- or five-coordinated nickel 334 S. Ciurli et al. / Coordination Chemistry Re6iews 190–192 (1999) 331–355 ions. Early EXAFS studies on JBU confirmed these results, and indicated the presence of pseudooctahedral Ni ions coordinated to three N atoms at 2.04 A,, two O atoms at 2.07 A,, and one O atom at 2.25 A,[45,46]. The presence of Ni-bound His residues was also suggested [45]. Later, new X-ray absorption spectroscopy data were interpreted with a model involving distorted octahedral Ni(II) ions bound to five or six (N,O) donors at an average distance of 2.06 A, [47]. Magnetic susceptibility experiments indicated that, in JBU, high spin octahedrally coordi- nated Ni(II) (S=1) ions are weakly antiferromagnetically coupled (J=−6.3 cm−1) [48]. This conclusion was subsequently disputed [49], but the diamagnetism resulting from binding of the competitive inhibitor b-mercaptoethanol (b-ME) [48], and the evidence that this binding involved a ligand exchange in the coordination sphere of nickel [47], suggested the presence, in the active site of JBU, of two closely spaced Ni(II) ions which, in the presence of b-ME, are strongly antiferromagneti- cally coupled through a bridging thiolate. This conclusion received further support from later EXAFS (extended X-ray absorption fine structure) studies, which indicated the appearance of a new peak in the Fourier transform upon addition of b-ME to JBU. This peak could be fitted using a model involving the presence of two Ni ions 3.26 A,apart [50]. This study also indicated the presence of His residues bound to pentacoordinated Ni(II) ions, with a coordination environment of the type Ni(His)x(N,O)5−x,
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